fperms 4755 /usr/bin/checkpassword-pam
could be added to the checkpassword-pam ebuild or at least an einfo saying to chmod the file manually.
Without the correct permissions one gets an error of type:
checkpassword-pam: Error setting supplementary groups for user x: Operation not permitted
checkpassword-pam: Exiting with status 111
This seems suspiciously similar to bug #76617 to me. Particularly comment 15/16.
*** Bug 265767 has been marked as a duplicate of this bug. ***